What settings affect the final number of samples in Cycles?
The reason your samples are so high is because you are using Square Samples. So instead of 12 you are using 144 (12x12) samples.

The square samples feature allows you to increase the sample numbers very fast.

This is how the author of this feature describes it on blenderartists.org

Basically brings Cycles more in line with Arnold. Noise in a path tracer takes longer to clear the longer a render goes on, which maps fairly closely to a n^2 curve. So basically, using squared samples allows every increase of 1 to equal a meaningful amount of noise reduction, and it allows an artist to have a very simple table of values stored in their head to clear noise for various common scene types